NMA on self-curated pdb files

[Former user]

Hi,

I would like to run a normal mode analysis on a selection of PDB files that are saved to my working directory. Is it possible to load a directory of PDB files and run the NMA? Any suggestions would be greatly appreciated!

[Xinqiu Yao]

Hi,

Yes, of course. Please go through bio3d tutorials, especially Beginning structure analysis and Ensemble normal mode analysis I (http://thegrantlab.org/bio3d/tutorials). In the tutorials, we download pdbs from database. In you case, you just need a list of file names (e.g., using list.files(). See help(list.files) for more information) and the proceed with pdbaln() etc.